Docker image cutadapt does not use pigz

I tested zarp on a local machine and when the rules with cutadapt ran, I noticed that they use gzip instead of the desired multithreaded pigz.

The docker image affected is: docker://zavolab/cutadapt:1.16-slim.

One quick fix to not waste resources is to set --set-threads remove_adapters_cutadapt=1 remove_polya_cutadapt=1 pe_remove_adapters_cutadapt=1 pe_remove_polya_cutadapt=1 in the snakemake call.

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@burri0000 Would it make sense to use a newer image? cutadapt:1.16 is quite old.

I don't know, this is the image also in the dev branch. At least I don't find any other cutadapt in our zavolab hub.

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In the image we have pigz though:

docker pull zavolab/cutadapt:1.16

downloads the image

docker run -it zavolab/cutadapt:1.16 pigz --version

gives pigz 2.3.4

docker run -it zavolab/cutadapt:1.16 which pigz

gives /usr/bin/pigz

Yes, but somehow it does not use it. I created a conda env with cutadapt=1.16 and pigz=2.4 and used that one instead of the singularity image on my local machine and then it worked as I saw that pigz was used.

I just checked with seff on the slurm by running remove_adapters_cutadapt on one individual file:

singularity image:

Nodes: 1
Cores per node: 8
CPU Utilized: 00:24:33
CPU Efficiency: 30.84% of 01:19:36 core-walltime
Job Wall-clock time: 00:09:57

conda env:

Nodes: 1
Cores per node: 8
CPU Utilized: 00:24:30
CPU Efficiency: 80.95% of 00:30:16 core-walltime
Job Wall-clock time: 00:03:47

ΟΚ thanks for reporting this. Can you please open an issue here (https://github.com/zavolanlab/Dockerfiles) and I will try to fix it

Also, please keep the current test files.

assigned to @gypas

@burri0000 Does the same happen with the slim version as well?

https://hub.docker.com/layers/zavolab/cutadapt/1.16-slim/images/sha256-556b050b777eb82264b3d8bc7bdd53355bdc214deb39c24f60345e0ce4e0c74e?context=explore

I only used the slim version, as this is the one we have in the Snakefile. But I could try with the normal version:

https://hub.docker.com/layers/zavolab/cutadapt/1.16/images/sha256-2846b9a53dd08011e8225113a9227561a533cfc682ab3ec070035f5f107332e6?context=explore

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So, this should be fixed via #149 (closed) . Closing for now.

closed